How to make the SNP density plot using hapmap file
Hi , have the Hapmap file hapmap_file.hmp.txt converted from vcf. I am trying to make a snp density plot like the given example. I want to convert my hapmap file into matrix or data frame using snpMatrix package. is there any other package or option to convert the file into matrix and please share some suggestions which packages are suitable to make the SNP density plot.
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rj.rezwan •
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here : CMplot
Thank you. I converted the
vcffile intohapmap.pedandhapmap.mapfile using plink. Later,hapmap.mapfile is used in Rpackage (CMplot)to draw the plot as given above.